Starting phenix.real_space_refine
on Wed Mar  4 05:20:12 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8ijx_35502/03_2026/8ijx_35502.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ijx_35502/03_2026/8ijx_35502.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ijx_35502/03_2026/8ijx_35502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ijx_35502/03_2026/8ijx_35502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ijx_35502/03_2026/8ijx_35502.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ijx_35502/03_2026/8ijx_35502.cif"
  }
  resolution = 2.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.091
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 9
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      1      5.21       5
     S      65      5.16       5
     Cl      1      4.86       5
     Be      1      3.05       5
     C    6573      2.51       5
     N    1654      2.21       5
     O    2241      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10545
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 983, 7633
          Classifications: {'peptide': 983}
          Link IDs: {'PTRANS': 47, 'TRANS': 935}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
    Chain: "B"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2142
          Classifications: {'peptide': 268}
          Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 273
          Unusual residues: {' MG': 1, 'PCW': 5, 'PZ0': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'PCW:plan-4': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "B"
      Number of atoms: 124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 124
          Unusual residues: {'CLR': 1, 'NAG': 3, 'PCW': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 259
          Classifications: {'water': 259}
          Link IDs: {None: 258}
    Chain: "B"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 114
          Classifications: {'water': 114}
          Link IDs: {None: 113}
  Time building chain proxies: 2.67, per 1000 atoms: 0.25
  Number of scatterers: 10545
  At special positions: 0
  Unit cell: (82.72, 94, 174.464, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     Cl      1     17.00
     S      65     16.00
     P       6     15.00
     Mg      1     11.99
     F       3      9.00
     O    2241      8.00
     N    1654      7.00
     C    6573      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 152 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 201 " - pdb=" SG  CYS B 262 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B 302 " - " ASN B  99 "
      " NAG B 303 " - " ASN B 130 "
      " NAG B 304 " - " ASN B 161 "
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 459.1 milliseconds
  

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2340

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 9 sheets defined
      50.6% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 84
    Processing helix  chain 'A' and resid 96 through 105
      removed outlier: 3.526A  pdb=" N   GLN A 104 " --> pdb=" O   LYS A 100 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU A 105 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 131
    Processing helix  chain 'A' and resid 135 through 169
      removed outlier: 3.952A  pdb=" N   LEU A 139 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 244 through 248
      removed outlier: 3.932A  pdb=" N   THR A 248 " --> pdb=" O   PRO A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 274 through 285
    Processing helix  chain 'A' and resid 291 through 322
    Processing helix  chain 'A' and resid 325 through 340
    Processing helix  chain 'A' and resid 344 through 363
      removed outlier: 3.711A  pdb=" N   LYS A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 374 through 379
    Processing helix  chain 'A' and resid 424 through 437
      removed outlier: 3.523A  pdb=" N   ARG A 432 " --> pdb=" O   ARG A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 454
    Processing helix  chain 'A' and resid 459 through 473
    Processing helix  chain 'A' and resid 475 through 482
    Processing helix  chain 'A' and resid 519 through 525
    Processing helix  chain 'A' and resid 542 through 557
    Processing helix  chain 'A' and resid 607 through 618
    Processing helix  chain 'A' and resid 629 through 640
    Processing helix  chain 'A' and resid 649 through 658
    Processing helix  chain 'A' and resid 660 through 664
    Processing helix  chain 'A' and resid 665 through 669
    Processing helix  chain 'A' and resid 676 through 681
      removed outlier: 3.549A  pdb=" N   ASP A 681 " --> pdb=" O   MET A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 694
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 727 through 729
      No H-bonds generated for 'chain 'A' and resid 727 through 729'
    Processing helix  chain 'A' and resid 730 through 737
    Processing helix  chain 'A' and resid 748 through 755
    Processing helix  chain 'A' and resid 765 through 791
      removed outlier: 4.043A  pdb=" N   LYS A 791 " --> pdb=" O   TYR A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 805
      Proline residue:  A 798  - end of helix
    Processing helix  chain 'A' and resid 812 through 822
    Processing helix  chain 'A' and resid 824 through 831
      removed outlier: 3.536A  pdb=" N   LEU A 831 " --> pdb=" O   PRO A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 839 through 843
      removed outlier: 3.758A  pdb=" N   LEU A 843 " --> pdb=" O   ILE A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 865
    Processing helix  chain 'A' and resid 865 through 885
    Processing helix  chain 'A' and resid 888 through 893
    Processing helix  chain 'A' and resid 895 through 901
    Processing helix  chain 'A' and resid 916 through 946
      removed outlier: 3.597A  pdb=" N   ALA A 941 " --> pdb=" O   MET A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 961 through 981
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 995 through 1000
    Processing helix  chain 'A' and resid 1001 through 1022
    Processing helix  chain 'A' and resid 1025 through 1032
      removed outlier: 3.602A  pdb=" N   TYR A1032 " --> pdb=" O   ASP A1028 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 66
    Processing helix  chain 'B' and resid 103 through 118
      removed outlier: 4.589A  pdb=" N   GLY B 108 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   LEU B 109 " --> pdb=" O   THR B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 121
      No H-bonds generated for 'chain 'B' and resid 119 through 121'
    Processing helix  chain 'B' and resid 155 through 164
      removed outlier: 6.733A  pdb=" N   ASN B 161 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   GLY B 164 " --> pdb=" O   ASN B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 223
      removed outlier: 4.166A  pdb=" N   THR B 223 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 190
      removed outlier: 11.912A  pdb=" N   GLN A 177 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
      removed outlier: 9.401A  pdb=" N   LYS A 203 " --> pdb=" O   GLN A 177 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   CYS A 258 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS A 221 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   GLU A 260 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   GLY A 219 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   THR A 262 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA A 217 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLN A 264 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   ASP A 211 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   CYS A 220 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190
      removed outlier: 11.912A  pdb=" N   GLN A 177 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
      removed outlier: 9.401A  pdb=" N   LYS A 203 " --> pdb=" O   GLN A 177 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   CYS A 258 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS A 221 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   GLU A 260 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   GLY A 219 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   THR A 262 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA A 217 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLN A 264 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   ASP A 211 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367
      removed outlier: 6.288A  pdb=" N   GLY A 740 " --> pdb=" O   MET A 757 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   LEU A 759 " --> pdb=" O   GLY A 740 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ALA A 742 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL A 721 " --> pdb=" O   ILE A 739 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   VAL A 741 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   VAL A 723 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   MET A 743 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLY A 725 " --> pdb=" O   MET A 743 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   VAL A 622 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 8.536A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   MET A 624 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.190A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS A 399 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   PHE A 594 " --> pdb=" O   GLN A 566 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   GLN A 566 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   THR A 503 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LYS A 485 " --> pdb=" O   THR A 503 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.190A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS A 399 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLY A 596 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908
    Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85
    Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 99
      removed outlier: 4.482A  pdb=" N   LEU B  94 " --> pdb=" O   GLU B 283 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1521 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2686
        1.33 -     1.45: 1797
        1.45 -     1.57: 5803
        1.57 -     1.69: 12
        1.69 -     1.81: 98
  Bond restraints: 10396
  Sorted by residual:
  bond pdb=" F3  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.529  1.765 -0.236 2.00e-02 2.50e+03 1.40e+02
  bond pdb=" F2  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.535  1.752 -0.217 2.00e-02 2.50e+03 1.17e+02
  bond pdb=" F1  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.542  1.752 -0.210 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" CG  BFD A 385 "
       pdb=" OD1 BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.269  1.446 -0.177 2.00e-02 2.50e+03 7.87e+01
  bond pdb=" C11 PCW A1105 "
       pdb=" O3  PCW A1105 "
    ideal  model  delta    sigma   weight residual
    1.326  1.455 -0.129 2.00e-02 2.50e+03 4.16e+01
  ... (remaining 10391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.32: 14004
        5.32 -    10.64: 65
       10.64 -    15.95: 4
       15.95 -    21.27: 2
       21.27 -    26.59: 3
  Bond angle restraints: 14078
  Sorted by residual:
  angle pdb=" C5  PCW A1104 "
        pdb=" N   PCW A1104 "
        pdb=" C8  PCW A1104 "
      ideal   model   delta    sigma   weight residual
     111.64   85.05   26.59 3.00e+00 1.11e-01 7.86e+01
  angle pdb=" C6  PCW A1104 "
        pdb=" N   PCW A1104 "
        pdb=" C8  PCW A1104 "
      ideal   model   delta    sigma   weight residual
     109.11   86.24   22.87 3.00e+00 1.11e-01 5.81e+01
  angle pdb=" C7  PCW A1104 "
        pdb=" N   PCW A1104 "
        pdb=" C8  PCW A1104 "
      ideal   model   delta    sigma   weight residual
     108.24   86.70   21.54 3.00e+00 1.11e-01 5.16e+01
  angle pdb=" F2  BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F3  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     112.60   95.51   17.09 3.00e+00 1.11e-01 3.25e+01
  angle pdb=" OD1 BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F1  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     102.38  118.43  -16.05 3.00e+00 1.11e-01 2.86e+01
  ... (remaining 14073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 6199
       35.81 -    71.63: 168
       71.63 -   107.44: 18
      107.44 -   143.25: 3
      143.25 -   179.07: 2
  Dihedral angle restraints: 6390
    sinusoidal: 2757
      harmonic: 3633
  Sorted by residual:
  dihedral pdb=" CA  GLY A 131 "
           pdb=" C   GLY A 131 "
           pdb=" N   ASP A 132 "
           pdb=" CA  ASP A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.38  -27.62     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CB  CYS B 131 "
           pdb=" SG  CYS B 131 "
           pdb=" SG  CYS B 152 "
           pdb=" CB  CYS B 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.65   39.35     1      1.00e+01 1.00e-02 2.18e+01
  dihedral pdb=" C33 PCW A1104 "
           pdb=" C31 PCW A1104 "
           pdb=" C32 PCW A1104 "
           pdb=" O2  PCW A1104 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -168.17   10.90 -179.07     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 6387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1290
       0.056 -    0.112: 246
       0.112 -    0.169: 23
       0.169 -    0.225: 5
       0.225 -    0.281: 3
  Chirality restraints: 1567
  Sorted by residual:
  chirality pdb=" C1  NAG B 302 "
            pdb=" ND2 ASN B  99 "
            pdb=" C2  NAG B 302 "
            pdb=" O5  NAG B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" C2  PCW A1101 "
            pdb=" C1  PCW A1101 "
            pdb=" C3  PCW A1101 "
            pdb=" O2  PCW A1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.58    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C13 CLR B 305 "
            pdb=" C12 CLR B 305 "
            pdb=" C14 CLR B 305 "
            pdb=" C17 CLR B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.70   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1564 not shown)

  Planarity restraints: 1786
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 303 "   -0.287 2.00e-02 2.50e+03   2.47e-01 7.62e+02
        pdb=" C7  NAG B 303 "    0.061 2.00e-02 2.50e+03
        pdb=" C8  NAG B 303 "    0.008 2.00e-02 2.50e+03
        pdb=" N2  NAG B 303 "    0.421 2.00e-02 2.50e+03
        pdb=" O7  NAG B 303 "   -0.204 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 302 "    0.158 2.00e-02 2.50e+03   1.32e-01 2.18e+02
        pdb=" C7  NAG B 302 "   -0.042 2.00e-02 2.50e+03
        pdb=" C8  NAG B 302 "    0.116 2.00e-02 2.50e+03
        pdb=" N2  NAG B 302 "   -0.215 2.00e-02 2.50e+03
        pdb=" O7  NAG B 302 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 304 "    0.140 2.00e-02 2.50e+03   1.15e-01 1.65e+02
        pdb=" C7  NAG B 304 "   -0.039 2.00e-02 2.50e+03
        pdb=" C8  NAG B 304 "    0.105 2.00e-02 2.50e+03
        pdb=" N2  NAG B 304 "   -0.183 2.00e-02 2.50e+03
        pdb=" O7  NAG B 304 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1783 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 166
        2.60 -     3.17: 8932
        3.17 -     3.75: 18209
        3.75 -     4.32: 25618
        4.32 -     4.90: 40020
  Nonbonded interactions: 92945
  Sorted by model distance:
  nonbonded pdb=" O   THR A 387 "
            pdb="MG    MG A1102 "
     model   vdw
     2.024 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O   HOH A1225 "
     model   vdw
     2.089 2.170
  nonbonded pdb=" OD2 ASP A 877 "
            pdb=" O   HOH A1201 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" F1  BFD A 385 "
            pdb="MG    MG A1102 "
     model   vdw
     2.170 2.120
  nonbonded pdb=" OE2 GLU A 686 "
            pdb=" O   HOH A1202 "
     model   vdw
     2.183 3.040
  ... (remaining 92940 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.930
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.236  10402  Z= 0.344
  Angle     :  0.927  26.591  14093  Z= 0.374
  Chirality :  0.045   0.281   1567
  Planarity :  0.008   0.247   1783
  Dihedral  : 15.625 179.067   4041
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  6.20 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.24), residues: 1244
  helix:  1.80 (0.22), residues: 578
  sheet:  0.28 (0.40), residues: 153
  loop :  0.24 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 278 
 TYR   0.015   0.001   TYR A 802 
 PHE   0.017   0.002   PHE B 284 
 TRP   0.012   0.001   TRP A 915 
 HIS   0.002   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00688 (10396)
  covalent geometry    : angle       0.92581 (14078)
  SS BOND              : bond        0.00491 (    3)
  SS BOND              : angle       0.68116 (    6)
  hydrogen bonds       : bond        0.12352 (  515)
  hydrogen bonds       : angle       5.53388 ( 1521)
  link_NAG-ASN         : bond        0.00322 (    3)
  link_NAG-ASN         : angle       1.86541 (    9)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 LYS cc_start: 0.8266 (tppt) cc_final: 0.7538 (tmtt)
REVERT: A  685 SER cc_start: 0.8093 (m) cc_final: 0.7647 (t)
REVERT: B   28 GLN cc_start: 0.6823 (tt0) cc_final: 0.6506 (tt0)
REVERT: B  131 CYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6599 (p)
REVERT: B  135 LYS cc_start: 0.7551 (mtpp) cc_final: 0.6757 (tptm)
  outliers start: 16
  outliers final: 10
  residues processed: 131
  average time/residue: 0.7463
  time to fit residues: 103.6566
Evaluate side-chains
  119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.3980
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0270
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 123 optimal weight:    0.1980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.5038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.172481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.127847 restraints weight = 8666.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.42
r_work: 0.3266 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.0655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10402  Z= 0.111
  Angle     :  0.532  10.358  14093  Z= 0.270
  Chirality :  0.043   0.279   1567
  Planarity :  0.004   0.048   1783
  Dihedral  : 14.196 172.632   1761
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.27 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.24), residues: 1244
  helix:  1.99 (0.21), residues: 582
  sheet:  0.61 (0.40), residues: 153
  loop :  0.41 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 439 
 TYR   0.014   0.001   TYR A 802 
 PHE   0.014   0.001   PHE B 284 
 TRP   0.010   0.001   TRP A 915 
 HIS   0.003   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (10396)
  covalent geometry    : angle       0.51347 (14078)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       0.65735 (    6)
  hydrogen bonds       : bond        0.04344 (  515)
  hydrogen bonds       : angle       4.38286 ( 1521)
  link_NAG-ASN         : bond        0.01041 (    3)
  link_NAG-ASN         : angle       5.51467 (    9)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: A  250 ASN cc_start: 0.8626 (p0) cc_final: 0.8345 (p0)
REVERT: A  358 LYS cc_start: 0.8568 (tppt) cc_final: 0.7989 (tmtt)
REVERT: A  477 MET cc_start: 0.6910 (mmt) cc_final: 0.6577 (mpt)
REVERT: A  685 SER cc_start: 0.8372 (m) cc_final: 0.8028 (t)
REVERT: B   28 GLN cc_start: 0.6908 (tt0) cc_final: 0.6544 (tt0)
REVERT: B   29 MET cc_start: 0.7353 (ttt) cc_final: 0.7049 (ttp)
REVERT: B  131 CYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6940 (p)
REVERT: B  135 LYS cc_start: 0.7882 (mtpp) cc_final: 0.7162 (tptm)
  outliers start: 16
  outliers final: 9
  residues processed: 120
  average time/residue: 0.7849
  time to fit residues: 99.5978
Evaluate side-chains
  119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 115 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 122 optimal weight:    0.7980
   chunk 112 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.171923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.127957 restraints weight = 8679.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.38
r_work: 0.3259 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.0759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10402  Z= 0.117
  Angle     :  0.513   6.502  14093  Z= 0.266
  Chirality :  0.043   0.252   1567
  Planarity :  0.004   0.043   1783
  Dihedral  : 13.933 172.966   1759
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  8.55 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.24), residues: 1244
  helix:  2.01 (0.21), residues: 582
  sheet:  0.60 (0.38), residues: 163
  loop :  0.47 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 328 
 TYR   0.016   0.001   TYR A 802 
 PHE   0.014   0.001   PHE B 284 
 TRP   0.010   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (10396)
  covalent geometry    : angle       0.50883 (14078)
  SS BOND              : bond        0.00396 (    3)
  SS BOND              : angle       0.60122 (    6)
  hydrogen bonds       : bond        0.04391 (  515)
  hydrogen bonds       : angle       4.21994 ( 1521)
  link_NAG-ASN         : bond        0.00413 (    3)
  link_NAG-ASN         : angle       2.46472 (    9)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  250 ASN cc_start: 0.8548 (p0) cc_final: 0.8330 (p0)
REVERT: A  358 LYS cc_start: 0.8554 (tppt) cc_final: 0.7979 (tmtt)
REVERT: A  477 MET cc_start: 0.6867 (mmt) cc_final: 0.6514 (mpt)
REVERT: B   29 MET cc_start: 0.7388 (ttt) cc_final: 0.7087 (ttp)
REVERT: B  131 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6633 (p)
REVERT: B  135 LYS cc_start: 0.7953 (mtpp) cc_final: 0.7211 (tptm)
  outliers start: 19
  outliers final: 12
  residues processed: 121
  average time/residue: 0.7855
  time to fit residues: 100.4615
Evaluate side-chains
  119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 113 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN
B 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.169936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.125324 restraints weight = 8638.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.39
r_work: 0.3224 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.0879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10402  Z= 0.153
  Angle     :  0.563   6.757  14093  Z= 0.294
  Chirality :  0.045   0.247   1567
  Planarity :  0.004   0.044   1783
  Dihedral  : 13.917 170.356   1757
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  9.21 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.24), residues: 1244
  helix:  1.87 (0.21), residues: 581
  sheet:  0.29 (0.37), residues: 171
  loop :  0.50 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 439 
 TYR   0.018   0.002   TYR A 802 
 PHE   0.015   0.002   PHE A 970 
 TRP   0.010   0.001   TRP A 915 
 HIS   0.006   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10396)
  covalent geometry    : angle       0.56096 (14078)
  SS BOND              : bond        0.00486 (    3)
  SS BOND              : angle       0.88295 (    6)
  hydrogen bonds       : bond        0.05045 (  515)
  hydrogen bonds       : angle       4.34559 ( 1521)
  link_NAG-ASN         : bond        0.00315 (    3)
  link_NAG-ASN         : angle       2.04274 (    9)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  287 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6895 (mm-30)
REVERT: A  358 LYS cc_start: 0.8584 (tppt) cc_final: 0.7978 (tmtt)
REVERT: A  455 ILE cc_start: 0.7850 (mm) cc_final: 0.7311 (tt)
REVERT: A  477 MET cc_start: 0.6889 (mmt) cc_final: 0.6616 (mpt)
REVERT: B  135 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7242 (tptm)
REVERT: B  160 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7169 (mm-40)
  outliers start: 20
  outliers final: 14
  residues processed: 122
  average time/residue: 0.7713
  time to fit residues: 99.6831
Evaluate side-chains
  125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 42 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0270
   overall best weight:    0.7238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.171527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.126642 restraints weight = 8609.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.42
r_work: 0.3248 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10402  Z= 0.118
  Angle     :  0.525   7.592  14093  Z= 0.271
  Chirality :  0.044   0.254   1567
  Planarity :  0.004   0.040   1783
  Dihedral  : 13.676 169.169   1757
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.24 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.24), residues: 1244
  helix:  2.00 (0.21), residues: 578
  sheet:  0.46 (0.38), residues: 163
  loop :  0.47 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 439 
 TYR   0.016   0.001   TYR A 802 
 PHE   0.014   0.001   PHE A 970 
 TRP   0.009   0.001   TRP A 915 
 HIS   0.003   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (10396)
  covalent geometry    : angle       0.51323 (14078)
  SS BOND              : bond        0.00275 (    3)
  SS BOND              : angle       0.78512 (    6)
  hydrogen bonds       : bond        0.04384 (  515)
  hydrogen bonds       : angle       4.15047 ( 1521)
  link_NAG-ASN         : bond        0.01305 (    3)
  link_NAG-ASN         : angle       4.43377 (    9)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A  358 LYS cc_start: 0.8542 (tppt) cc_final: 0.7950 (tmtt)
REVERT: A  477 MET cc_start: 0.6773 (mmt) cc_final: 0.6564 (mpt)
REVERT: B   29 MET cc_start: 0.7362 (ttt) cc_final: 0.7025 (ttp)
REVERT: B  131 CYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7133 (p)
REVERT: B  135 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7207 (tptm)
  outliers start: 19
  outliers final: 13
  residues processed: 121
  average time/residue: 0.7823
  time to fit residues: 100.3798
Evaluate side-chains
  121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0970
   chunk 38 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 76 optimal weight:    0.6980
   chunk 118 optimal weight:    0.0070
   chunk 119 optimal weight:    0.8980
   overall best weight:    0.4396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.173264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.128429 restraints weight = 8726.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.47
r_work: 0.3272 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10402  Z= 0.101
  Angle     :  0.492   7.331  14093  Z= 0.252
  Chirality :  0.043   0.262   1567
  Planarity :  0.004   0.038   1783
  Dihedral  : 13.204 177.660   1757
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.71 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.24), residues: 1244
  helix:  2.19 (0.21), residues: 571
  sheet:  0.43 (0.37), residues: 168
  loop :  0.43 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 439 
 TYR   0.013   0.001   TYR A 802 
 PHE   0.015   0.001   PHE A 970 
 TRP   0.009   0.001   TRP A 915 
 HIS   0.003   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 (10396)
  covalent geometry    : angle       0.48111 (14078)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       0.81571 (    6)
  hydrogen bonds       : bond        0.03886 (  515)
  hydrogen bonds       : angle       3.97405 ( 1521)
  link_NAG-ASN         : bond        0.01168 (    3)
  link_NAG-ASN         : angle       4.09122 (    9)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  287 GLU cc_start: 0.7420 (pm20) cc_final: 0.6903 (mm-30)
REVERT: A  358 LYS cc_start: 0.8550 (tppt) cc_final: 0.7985 (tmtt)
REVERT: A  415 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7653 (mm110)
REVERT: A  686 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7051 (tp30)
REVERT: B   29 MET cc_start: 0.7454 (ttt) cc_final: 0.7145 (ttp)
REVERT: B  131 CYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7038 (p)
REVERT: B  135 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7097 (tptm)
  outliers start: 19
  outliers final: 12
  residues processed: 123
  average time/residue: 0.7744
  time to fit residues: 100.8232
Evaluate side-chains
  120 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.169623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.125398 restraints weight = 8521.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.40
r_work: 0.3222 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10402  Z= 0.175
  Angle     :  0.600   8.664  14093  Z= 0.311
  Chirality :  0.047   0.278   1567
  Planarity :  0.005   0.039   1783
  Dihedral  : 13.760 178.356   1757
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.71 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.23), residues: 1244
  helix:  1.83 (0.21), residues: 579
  sheet:  0.19 (0.37), residues: 171
  loop :  0.51 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 439 
 TYR   0.020   0.002   TYR A 802 
 PHE   0.018   0.002   PHE A 970 
 TRP   0.008   0.002   TRP B 106 
 HIS   0.005   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10396)
  covalent geometry    : angle       0.58772 (14078)
  SS BOND              : bond        0.00463 (    3)
  SS BOND              : angle       0.76887 (    6)
  hydrogen bonds       : bond        0.05274 (  515)
  hydrogen bonds       : angle       4.34205 ( 1521)
  link_NAG-ASN         : bond        0.01553 (    3)
  link_NAG-ASN         : angle       4.76027 (    9)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  287 GLU cc_start: 0.7417 (pm20) cc_final: 0.6968 (mm-30)
REVERT: A  453 LYS cc_start: 0.8015 (mttp) cc_final: 0.7678 (mtpm)
REVERT: B   29 MET cc_start: 0.7352 (ttt) cc_final: 0.7037 (ttp)
REVERT: B  131 CYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7099 (p)
REVERT: B  135 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7264 (tptm)
REVERT: B  256 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7831 (ttm-80)
  outliers start: 18
  outliers final: 14
  residues processed: 122
  average time/residue: 0.7807
  time to fit residues: 100.9148
Evaluate side-chains
  122 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 79 optimal weight:    0.0670
   chunk 107 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 121 optimal weight:    0.3980
   chunk 78 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.4316

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
B 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.172540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.127888 restraints weight = 8595.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.46
r_work: 0.3263 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10402  Z= 0.105
  Angle     :  0.505   9.920  14093  Z= 0.259
  Chirality :  0.043   0.266   1567
  Planarity :  0.004   0.036   1783
  Dihedral  : 13.136 173.717   1757
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.09 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.24), residues: 1244
  helix:  2.07 (0.21), residues: 577
  sheet:  0.40 (0.37), residues: 163
  loop :  0.49 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 256 
 TYR   0.014   0.001   TYR A 802 
 PHE   0.015   0.001   PHE A 970 
 TRP   0.009   0.001   TRP A 915 
 HIS   0.003   0.001   HIS A 629 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (10396)
  covalent geometry    : angle       0.48964 (14078)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       0.72073 (    6)
  hydrogen bonds       : bond        0.04042 (  515)
  hydrogen bonds       : angle       4.02450 ( 1521)
  link_NAG-ASN         : bond        0.01242 (    3)
  link_NAG-ASN         : angle       4.96473 (    9)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A  287 GLU cc_start: 0.7427 (pm20) cc_final: 0.6909 (mm-30)
REVERT: A  358 LYS cc_start: 0.8560 (tppt) cc_final: 0.7991 (tmtt)
REVERT: A  686 GLU cc_start: 0.8087 (mt-10) cc_final: 0.6894 (tp30)
REVERT: B   29 MET cc_start: 0.7429 (ttt) cc_final: 0.7093 (ttp)
REVERT: B  131 CYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7023 (p)
REVERT: B  135 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7204 (tptm)
REVERT: B  256 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7855 (ttm-80)
  outliers start: 17
  outliers final: 13
  residues processed: 120
  average time/residue: 0.7894
  time to fit residues: 100.2746
Evaluate side-chains
  122 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0570
   overall best weight:    0.9700

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
B 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.170799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.126623 restraints weight = 8580.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 1.33
r_work: 0.3247 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10402  Z= 0.132
  Angle     :  0.543   9.989  14093  Z= 0.280
  Chirality :  0.045   0.248   1567
  Planarity :  0.004   0.037   1783
  Dihedral  : 13.157 172.124   1757
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.90 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.24), residues: 1244
  helix:  1.96 (0.21), residues: 577
  sheet:  0.19 (0.37), residues: 171
  loop :  0.52 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 256 
 TYR   0.017   0.002   TYR A 802 
 PHE   0.019   0.002   PHE A 970 
 TRP   0.009   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10396)
  covalent geometry    : angle       0.52840 (14078)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       0.59236 (    6)
  hydrogen bonds       : bond        0.04639 (  515)
  hydrogen bonds       : angle       4.15590 ( 1521)
  link_NAG-ASN         : bond        0.01172 (    3)
  link_NAG-ASN         : angle       4.94323 (    9)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  358 LYS cc_start: 0.8553 (tppt) cc_final: 0.7966 (tmtt)
REVERT: A  453 LYS cc_start: 0.8004 (mttp) cc_final: 0.7667 (mtpm)
REVERT: A  686 GLU cc_start: 0.8105 (mt-10) cc_final: 0.6930 (tp30)
REVERT: B   29 MET cc_start: 0.7433 (ttt) cc_final: 0.7105 (ttp)
REVERT: B  131 CYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7032 (p)
REVERT: B  135 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7235 (tptm)
REVERT: B  256 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7827 (ttm-80)
  outliers start: 18
  outliers final: 13
  residues processed: 123
  average time/residue: 0.7254
  time to fit residues: 94.6435
Evaluate side-chains
  120 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 108 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0980
   chunk 70 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 122 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
B 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.171868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.127101 restraints weight = 8557.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.41
r_work: 0.3256 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.1148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10402  Z= 0.115
  Angle     :  0.522  10.235  14093  Z= 0.268
  Chirality :  0.044   0.280   1567
  Planarity :  0.004   0.035   1783
  Dihedral  : 12.977 170.806   1757
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.28 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.24), residues: 1244
  helix:  2.01 (0.21), residues: 578
  sheet:  0.41 (0.37), residues: 163
  loop :  0.51 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 256 
 TYR   0.015   0.001   TYR A 802 
 PHE   0.018   0.001   PHE A 970 
 TRP   0.009   0.001   TRP B  39 
 HIS   0.003   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (10396)
  covalent geometry    : angle       0.50666 (14078)
  SS BOND              : bond        0.00351 (    3)
  SS BOND              : angle       0.63891 (    6)
  hydrogen bonds       : bond        0.04296 (  515)
  hydrogen bonds       : angle       4.06248 ( 1521)
  link_NAG-ASN         : bond        0.01171 (    3)
  link_NAG-ASN         : angle       5.05506 (    9)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 LYS cc_start: 0.8563 (tppt) cc_final: 0.7985 (tmtt)
REVERT: A  686 GLU cc_start: 0.8048 (mt-10) cc_final: 0.6914 (tp30)
REVERT: B   29 MET cc_start: 0.7476 (ttt) cc_final: 0.7146 (ttp)
REVERT: B  131 CYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6944 (p)
REVERT: B  135 LYS cc_start: 0.7987 (mtpp) cc_final: 0.7224 (tptm)
REVERT: B  256 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7837 (ttm-80)
  outliers start: 15
  outliers final: 13
  residues processed: 120
  average time/residue: 0.7785
  time to fit residues: 98.9026
Evaluate side-chains
  119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 123 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 109 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0060
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.6396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
B 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.172144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127186 restraints weight = 8657.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.45
r_work: 0.3254 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10402  Z= 0.112
  Angle     :  0.517  10.285  14093  Z= 0.266
  Chirality :  0.044   0.263   1567
  Planarity :  0.004   0.035   1783
  Dihedral  : 12.783 169.691   1757
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.09 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.24), residues: 1244
  helix:  2.03 (0.21), residues: 578
  sheet:  0.39 (0.37), residues: 163
  loop :  0.52 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 256 
 TYR   0.015   0.001   TYR A 802 
 PHE   0.018   0.001   PHE A 970 
 TRP   0.011   0.001   TRP B  39 
 HIS   0.003   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (10396)
  covalent geometry    : angle       0.50094 (14078)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       0.56531 (    6)
  hydrogen bonds       : bond        0.04234 (  515)
  hydrogen bonds       : angle       4.03204 ( 1521)
  link_NAG-ASN         : bond        0.01155 (    3)
  link_NAG-ASN         : angle       5.02135 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6008.83 seconds
wall clock time: 102 minutes 32.56 seconds (6152.56 seconds total)